Background Chlamydia trachomatis is a gram negative bacteria, which involve in sexually transmitted disease. This study was aimed to detect C. trachomatis by molecular methods and to evaluate Chlamydial infections in women suffering from primary and secondary infertility with special emphasis. Method 200 endocervical cytobrush were obtained from 200 infertile women having primary and secondary infertility. The work has been carried out at Basra Maternity and Child Hospital for molecular analysis of C. trachomatis . The primer CT1& CT4 w used to investigate the 144bp of MOMP of C. trachomatis in the endocervical brush samples. Results Out of 200 infertile women 96(48%) were positive for C. trachomatis by PCR. Conclusion The percentage of C.trachomatis in primary infertile women with blocked tubes was higher than women with patent tubes and also higher than C. trachomatis in secondary infertile women with both blocked and patent tubes.